jbrowse-plugin-msaview 2.0.6 → 2.1.0

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const EnsemblGeneTree: ({ model, feature, handleClose, }: {
+    model: AbstractTrackModel;
+    feature: Feature;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default EnsemblGeneTree;

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js

@@ -0,0 +1,81 @@
+import React, { useEffect, useState } from 'react';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { getContainingView, getSession, } from '@jbrowse/core/util';
+import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView';
+import { geneTreeFetcher } from './ensemblGeneTreeUtils';
+import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+});
+const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
+    const session = getSession(model);
+    const view = getContainingView(model);
+    const { classes } = useStyles();
+    const [error, setError] = useState();
+    const [treeData, setTreeData] = useState();
+    const [isTreeLoading, setIsTreeLoading] = useState(false);
+    const [treeError, setTreeError] = useState();
+    const options = getTranscriptFeatures(feature);
+    const [userSelection, setUserSelection] = useState(getId(options[0]));
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                setIsTreeLoading(true);
+                const result = await geneTreeFetcher(userSelection);
+                setTreeData(result);
+            }
+            catch (e) {
+                console.error(e);
+                setTreeError(e);
+            }
+            finally {
+                setIsTreeLoading(false);
+            }
+        })();
+    }, [userSelection]);
+    const loadingMessage = isTreeLoading
+        ? 'Loading tree data from Ensembl GeneTree'
+        : undefined;
+    const e = treeError ?? error;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            e ? React.createElement(ErrorMessage, { error: e }) : null,
+            loadingMessage ? React.createElement(LoadingEllipses, { message: loadingMessage }) : null,
+            React.createElement(Typography, null, "Load data from Ensembl GeneTree"),
+            React.createElement(TextField, { select: true, label: "Choose isoform to view MSA for", value: userSelection, onChange: event => {
+                    setUserSelection(event.target.value);
+                } }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() }, getTranscriptDisplayName(val)))))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
+                    try {
+                        if (!treeData) {
+                            return;
+                        }
+                        setError(undefined);
+                        ensemblGeneTreeLaunchView({
+                            feature,
+                            view,
+                            session,
+                            newViewTitle: getGeneDisplayName(feature),
+                            data: treeData,
+                        });
+                        handleClose();
+                    }
+                    catch (e) {
+                        console.error(e);
+                        setError(e);
+                    }
+                } }, "Submit"),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
+});
+export default EnsemblGeneTree;
+//# sourceMappingURL=EnsemblGeneTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.d.ts

@@ -0,0 +1,13 @@
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export declare function ensemblGeneTreeLaunchView({ session, newViewTitle, view, feature, data, }: {
+    session: AbstractSessionModel;
+    newViewTitle: string;
+    view: LinearGenomeViewModel;
+    feature: Feature;
+    data: {
+        tree: string;
+        msa: string;
+        treeMetadata: string;
+    };
+}): void;

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js

@@ -0,0 +1,18 @@
+export function ensemblGeneTreeLaunchView({ session, newViewTitle, view, feature, data, }) {
+    session.addView('MsaView', {
+        type: 'MsaView',
+        displayName: newViewTitle,
+        treeAreaWidth: 200,
+        treeWidth: 100,
+        drawNodeBubbles: false,
+        labelsAlignRight: true,
+        showBranchLen: false,
+        colWidth: 10,
+        rowHeight: 12,
+        colorSchemeName: 'percent_identity_dynamic',
+        data,
+        connectedViewId: view.id,
+        connectedFeature: feature.toJSON(),
+    });
+}
+//# sourceMappingURL=ensemblGeneTreeLaunchView.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts

@@ -0,0 +1,5 @@
+export declare function geneTreeFetcher(id2: string): Promise<{
+    tree: string;
+    msa: string;
+    treeMetadata: string;
+}>;

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js

@@ -0,0 +1,35 @@
+import { fetchWithLocalStorageCache, jsonfetch, textfetch } from './util';
+function gatherSequencesFromTree(tree, arr = []) {
+    if (tree.children) {
+        for (const child of tree.children) {
+            if (child.sequence) {
+                const id = child.sequence.id[0]?.accession;
+                if (id) {
+                    arr.push({
+                        id,
+                        seq: child.sequence.mol_seq.seq,
+                        species: child.taxonomy.common_name || child.taxonomy.scientific_name,
+                        genomicLocString: child.sequence.mol_seq.location,
+                    });
+                }
+            }
+            gatherSequencesFromTree(child, arr);
+        }
+    }
+    return arr;
+}
+const base = 'https://rest.ensembl.org';
+export async function geneTreeFetcher(id2) {
+    const id = id2.replace(/\..*/, '');
+    const { species } = await fetchWithLocalStorageCache(`${id}-ensembl`, () => jsonfetch(`${base}/lookup/id/${id}?content-type=application/json`));
+    const treeBase = `${base}/genetree/member/id/${species}/${id}`;
+    const msa = await fetchWithLocalStorageCache(`${id}-msa`, () => jsonfetch(`${treeBase}?content-type=application/json;aligned=1;sequence=pep`));
+    const tree = await fetchWithLocalStorageCache(`${id}-tree`, () => textfetch(`${treeBase}?nh_format=simple;content-type=text/x-nh`));
+    const res = gatherSequencesFromTree(msa.tree);
+    return {
+        tree,
+        msa: res.map(r => `>${r.id}\n${r.seq}`).join('\n'),
+        treeMetadata: JSON.stringify(Object.fromEntries(res.map(r => [r.id, { genome: r.species }]))),
+    };
+}
+//# sourceMappingURL=ensemblGeneTreeUtils.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/fetchGeneList.d.ts

@@ -0,0 +1 @@
+export declare function fetchGeneList(): Promise<string[]>;

package/dist/LaunchMsaView/components/EnsemblGeneTree/fetchGeneList.js

@@ -0,0 +1,12 @@
+export async function fetchGeneList() {
+    const res = await fetch('https://jbrowse.org/demos/msaview/knownCanonical/list.txt');
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`);
+    }
+    const result = await res.text();
+    return result
+        .split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f);
+}
+//# sourceMappingURL=fetchGeneList.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/fetchGeneList.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts

@@ -0,0 +1,4 @@
+export declare function jsonfetch<T>(url: string, arg?: RequestInit): Promise<T>;
+export declare function textfetch(url: string, arg?: RequestInit): Promise<string>;
+export declare function fetchWithLocalStorageCache<T>(key: string, fetchFn: () => Promise<T>): Promise<T>;
+export declare function unzipfetch(url: string, arg?: RequestInit): Promise<string>;

package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js

@@ -0,0 +1,38 @@
+import { ungzip } from 'pako';
+export async function jsonfetch(url, arg) {
+    const res = await fetch(url, arg);
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} from ${url}: ${await res.text()}`);
+    }
+    return res.json();
+}
+export async function textfetch(url, arg) {
+    const res = await fetch(url, arg);
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} from ${url}`);
+    }
+    return res.text();
+}
+export async function fetchWithLocalStorageCache(key, fetchFn) {
+    const cachedData = localStorage.getItem(key);
+    if (cachedData) {
+        try {
+            return JSON.parse(cachedData);
+        }
+        catch (error) {
+            console.error(`Error parsing cached data for ${key}:`, error);
+            // Continue to fetch fresh data if parsing fails
+        }
+    }
+    const data = await fetchFn();
+    localStorage.setItem(key, JSON.stringify(data));
+    return data;
+}
+export async function unzipfetch(url, arg) {
+    const res = await fetch(url, arg);
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} from ${url}: ${await res.text()}`);
+    }
+    return ungzip(await res.arrayBuffer(), { to: 'string' });
+}
+//# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js

@@ -1,24 +1,30 @@
 import React, { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
-import { Box, Tab, Tabs } from '@mui/material';
+import { Tab, Tabs } from '@mui/material';
+import EnsemblGeneTree from './EnsemblGeneTree/EnsemblGeneTree';
+import MSALoader from './MSALoader/MSALoader';
 import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery';
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
-import CustomTabPanel from './TabUtils';
-import { a11yProps } from './tabUtil';
+import TabPanel from './TabPanel';
 export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
     const [value, setValue] = useState(0);
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", onClose: () => {
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", open: true, onClose: () => {
             handleClose();
-        }, open: true },
-        React.createElement(Box, { sx: { borderBottom: 1, borderColor: 'divider' } },
-            React.createElement(Tabs, { value: value, onChange: (_, val) => {
-                    setValue(val);
-                } },
-                React.createElement(Tab, { label: "NCBI BLAST query", ...a11yProps(0) }),
-                React.createElement(Tab, { label: "UCSC 100-way dataset", ...a11yProps(1) }))),
-        React.createElement(CustomTabPanel, { value: value, index: 0 },
+        } },
+        React.createElement(Tabs, { value: value, onChange: (_, val) => {
+                setValue(val);
+            } },
+            React.createElement(Tab, { label: "NCBI BLAST query", value: 0 }),
+            React.createElement(Tab, { label: "UCSC 100-way dataset", value: 1 }),
+            React.createElement(Tab, { label: "Ensembl GeneTree", value: 2 }),
+            React.createElement(Tab, { label: "Manually open MSA", value: 3 })),
+        React.createElement(TabPanel, { value: value, index: 0 },
             React.createElement(NewNcbiBlastQueryPanel, { handleClose: handleClose, feature: feature, model: model })),
-        React.createElement(CustomTabPanel, { value: value, index: 1 },
-            React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose }))));
+        React.createElement(TabPanel, { value: value, index: 1 },
+            React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose })),
+        React.createElement(TabPanel, { value: value, index: 2 },
+            React.createElement(EnsemblGeneTree, { model: model, feature: feature, handleClose: handleClose })),
+        React.createElement(TabPanel, { value: value, index: 3 },
+            React.createElement(MSALoader, { model: model, feature: feature, handleClose: handleClose }))));
 }
 //# sourceMappingURL=LaunchMsaViewDialog.js.map

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/MSALoader/MSALoader.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const PreLoadedMSA: ({ model, feature, handleClose, }: {
+    model: AbstractTrackModel;
+    feature: Feature;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default PreLoadedMSA;

package/dist/LaunchMsaView/components/MSALoader/MSALoader.js

@@ -0,0 +1,94 @@
+import React, { useEffect, useState } from 'react';
+import { FileSelector } from '@jbrowse/core/ui';
+import { getContainingView, getSession, } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { Button, DialogActions, DialogContent } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { fetchGeneList } from './fetchGeneList';
+import { preCalculatedLaunchView } from './preCalculatedLaunchView';
+import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+});
+const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClose, }) {
+    const session = getSession(model);
+    const view = getContainingView(model);
+    const { classes } = useStyles();
+    const [, setError] = useState();
+    const [geneNameList, setGeneNameList] = useState();
+    const [fileLocation, setFileLocation] = useState();
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                const data = await fetchGeneList();
+                setGeneNameList(data);
+                const set = new Set(data);
+                const options = getTranscriptFeatures(feature);
+                const ret = options.find(val => set.has(getId(val)));
+                if (ret) {
+                    setUserSelection(getId(ret));
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [feature]);
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                if (fileLocation) {
+                    await openLocation(fileLocation).readFile();
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [fileLocation, feature]);
+    const set = new Set(geneNameList);
+    const options = getTranscriptFeatures(feature);
+    const ret = options.find(val => set.has(getId(val)));
+    const [userSelection, setUserSelection] = useState(getId(options[0]));
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            React.createElement(FileSelector, { location: fileLocation, setLocation: setFileLocation })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        try {
+                            if (!ret) {
+                                return;
+                            }
+                            await preCalculatedLaunchView({
+                                userSelection,
+                                session,
+                                newViewTitle: getGeneDisplayName(ret),
+                                view,
+                                feature: ret,
+                            });
+                            handleClose();
+                        }
+                        catch (e) {
+                            console.error(e);
+                            setError(e);
+                        }
+                    })();
+                } }, "Submit"),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
+});
+export default PreLoadedMSA;
+//# sourceMappingURL=MSALoader.js.map

package/dist/LaunchMsaView/components/MSALoader/MSALoader.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.d.ts

@@ -0,0 +1 @@
+export declare function fetchGeneList(): Promise<string[]>;

package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js

@@ -0,0 +1,12 @@
+export async function fetchGeneList() {
+    const res = await fetch('https://jbrowse.org/demos/msaview/knownCanonical/list.txt');
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`);
+    }
+    const result = await res.text();
+    return result
+        .split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f);
+}
+//# sourceMappingURL=fetchGeneList.js.map

package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fetchGeneList.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/MSALoader/fetchGeneList.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,GAAG,GAAG,MAAM,KAAK,CACrB,2DAA2D,CAC5D,CAAA;IACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,kBAAkB,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IACzE,CAAC;IACD,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;IAC/B,OAAO,MAAM;SACV,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrB,CAAC"}

package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.d.ts

@@ -0,0 +1,9 @@
+import { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export declare function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }: {
+    session: AbstractSessionModel;
+    userSelection: string;
+    newViewTitle: string;
+    view: LinearGenomeViewModel;
+    feature: Feature;
+}): Promise<void>;

package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js

@@ -0,0 +1,36 @@
+import { ungzip } from 'pako';
+async function myfetch(url) {
+    const res = await fetch(url);
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} fetching ${await res.text()}`);
+    }
+    const data = await res.arrayBuffer();
+    return new TextDecoder().decode(ungzip(data));
+}
+export async function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }) {
+    const d = await myfetch(`https://jbrowse.org/demos/msaview/knownCanonical/${userSelection}.mfa.gz`);
+    session.addView('MsaView', {
+        type: 'MsaView',
+        displayName: newViewTitle,
+        treeAreaWidth: 200,
+        treeWidth: 100,
+        drawNodeBubbles: false,
+        labelsAlignRight: true,
+        showBranchLen: false,
+        colWidth: 10,
+        rowHeight: 12,
+        colorSchemeName: 'percent_identity_dynamic',
+        treeFilehandle: {
+            uri: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.nh',
+        },
+        treeMetadataFilehandle: {
+            uri: 'https://s3.amazonaws.com/jbrowse.org/demos/app/species.json',
+        },
+        data: {
+            msa: d,
+        },
+        connectedViewId: view.id,
+        connectedFeature: feature.toJSON(),
+    });
+}
+//# sourceMappingURL=preCalculatedLaunchView.js.map

package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.d.ts

@@ -1,23 +1,15 @@
-import { Feature } from '@jbrowse/core/util';
-export interface Feat {
-    start: number;
-    end: number;
-    type: string;
-}
+import type { Feat } from './types';
+import type { Feature } from '@jbrowse/core/util';
 export declare function stitch(subfeats: Feat[], sequence: string): string;
 export declare function calculateProteinSequence({ cds, sequence, codonTable, }: {
     cds: Feat[];
     sequence: string;
     codonTable: Record<string, string>;
 }): string;
-export declare function revlist(list: {
-    start: number;
-    end: number;
-    type: string;
-}[], seqlen: number): {
+export declare function revlist(list: Feat[], seqlen: number): {
     start: number;
     end: number;
-    type: string;
+    type?: string;
 }[];
 export declare function dedupe(list: Feat[]): Feat[];
 export declare function getProteinSequence({ selectedTranscript, seq, }: {

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js

@@ -29,16 +29,15 @@ export function dedupe(list) {
     return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
 }
 export function getProteinSequence({ selectedTranscript, seq, }) {
-    // @ts-expect-error
     const f = selectedTranscript.toJSON();
     const cds = dedupe(f.subfeatures
-        .sort((a, b) => a.start - b.start)
+        ?.sort((a, b) => a.start - b.start)
         .map(sub => ({
         ...sub,
         start: sub.start - f.start,
         end: sub.end - f.start,
     }))
-        .filter(f => f.type === 'CDS'));
+        .filter(f => f.type === 'CDS') || []);
     return calculateProteinSequence({
         cds: f.strand === -1 ? revlist(cds, seq.length) : cds,
         sequence: f.strand === -1 ? revcom(seq) : seq,

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/fetchSeq.d.ts

@@ -0,0 +1,8 @@
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+export declare function fetchSeq({ start, end, refName, session, assemblyName, }: {
+    start: number;
+    end: number;
+    refName: string;
+    assemblyName: string;
+    session: AbstractSessionModel;
+}): Promise<string>;

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/fetchSeq.js

@@ -0,0 +1,23 @@
+import { getConf } from '@jbrowse/core/configuration';
+export async function fetchSeq({ start, end, refName, session, assemblyName, }) {
+    const { assemblyManager, rpcManager } = session;
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        throw new Error('assembly not found');
+    }
+    const sessionId = 'getSequence';
+    const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+        sessionId,
+        regions: [
+            {
+                start,
+                end,
+                refName: assembly.getCanonicalRefName(refName),
+                assemblyName,
+            },
+        ],
+    }));
+    return feats[0]?.get('seq') ?? '';
+}
+//# sourceMappingURL=fetchSeq.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/fetchSeq.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/types.d.ts

@@ -0,0 +1,10 @@
+export interface Feat {
+    start: number;
+    end: number;
+    type?: string;
+}
+export interface SeqState {
+    seq: string;
+    upstream?: string;
+    downstream?: string;
+}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/types.ts"],"names":[],"mappings":""}